Ring species provide important evidence of evolution in that they illustrate what happens over time as populations genetically diverge, and are special because they represent in living populations what normally happens over time between long deceased ancestor populations and living populations, in which the intermediates have become extinct. Richard Dawkins observes that ring species "are only showing us in the spatial dimension something that must always happen in the time dimension."

Ring species also present an interesting case of the species problem, for those who seek to divide the living world into discrete species. After all, all that distinguishes a ring species from two separate species is the existence of the connecting populations - if enough of the connecting populations within the ring perish to sever the breeding connection, the ring species' distal populations will be recognized as two distinct species.

I'd take this opportunity to present my own kind of ring species, which actually isn't a ring in a geographical sense, but it presents a continuum between intraspecific and interspecific differentiation:The pea aphid complex.

Ask him to define 'information' and give examples of it's measurement in biology.

...and give examples of it's measurement in biology.

First, ask IDers why we should even care about "information" in evolutionary biology.

If the IDiots were, indeed, correct about how evolution is affected by 'information' and changes thereof and yada yada yada, then it would be pretty friggin' obvious that we should care about 'information' in evolutionary biology. Of course, if that were the case, then the IDiots' position would be based on fact rather than unshakable religious dogma, and they would be able to answer questions like 'which nucleotide sequence has more information in it?"

His thesis is that two distinct traits are coextensive if and only if whatever has one has both. For polar bears, the traits `being white' and `matching the environment' are clearly different traits; grasshoppers have the second but not the first. Since all polar bears have both, a theory of `selection for` has to decide which of these traits were selected for in polar bears; which, he says the Darwinian account of adaptation can't do. So there must be something wrong with the Darwinian account of adaptation. Except for being succinct, this is just a standard case of free-riding: either being white free-rides on matching the environment or matching the environment free-rides on being white. Which does the adaptationist prefer; and what is his argument for preferring it?

<a href="http://wfsc.tamu.edu/faculty/tdewitt/WFSC622/Arnold%20chapter.pdf">Lande and Arnold </a> would certainly argue that that is possible, and indeed, one of the uses that they support for G-matrix multiple regression analysis is to find out on what traits selection was "directly" working versus what traits are changing because of correlational effects.

But this use, demands that one know that G is stable through the changes in the population. And that is not only not known, but known to be unlikely in natural populations.

Of course, if one has additional information about the population -- especially the kinds of 'hands on' information that provides useful clues to the biological pathways involved -- then these kinds of G-based analyses can provide some additional insights. And that, is how I think that e.g., Steve Arnold really uses G-matrices when he uses them to study natural populations. Much of that field-based understanding of the systems in questions gets hidden in the written work, but it is what makes him confident that his results make sense.

So this guy redefines 'traits' for us. I see.

A trait is a distinct variant of a phenotypic character of an organism that may be inherited, environmentally determined or be a combination of the two.[1] For example, eye color is a character or abstraction of an attribute, while blue, brown and hazel are traits.

"Matching the environment" is NOT a trait. It is a consequence of a trait. For example, the an Arctic fox, in its winter coat would match the environment in winter, but would not do so in the summer.

Since his entire basis is wrong, then everything he says after that (i.e. Darwinian evolution can't do something) is wrong too. Not because Darwinian evolution can do what he wants, but because what he wants is nonsensical.

This is exactly like the requirement that creationists often use to say, "We must have a complete fossil record." Knowing that it is impossible AND not required for anyone except them.

Again, you can argue all the math, facts, requirements, etc you want to. If your initial claim or assumption is nonsense, then everything after that is a complete waste of time.

--------------Ignored by those who can't provide evidence for their claims.

If the IDiots were, indeed, correct about how evolution is affected by 'information' and changes thereof and yada yada yada, then it would be pretty friggin' obvious that we should care about 'information' in evolutionary biology.

It's not obvious at all to me. Even if a defined measure of information content in the genome cannot increase by means of mutation and natural selection, why should be care? The postulates of natural selection say nothing about "information".Mutations produce alleles controlling different heritable phenotypes, we know that. All phenotypes, hence the alleles, don't have equal reproductive success in a given environment. We know that too. That's all that's needed.

To me all this information stuff is just as bogus as the argument based on the SLoT.

About the polar bear example... Starbuck's post isn't only bogus, it came out of nowhere, beginning with a "His" that refers to god knows who. Not sure what to make of this.

If the IDiots were, indeed, correct about how evolution is affected by 'information' and changes thereof and yada yada yada, then it would be pretty friggin' obvious that we should care about 'information' in evolutionary biology.

It's not obvious at all to me. Even if a defined measure of information content in the genome cannot increase by means of mutation and natural selection, why should we care?

Because when an IDiot/Creationist makes noise about what can or cannot be done by mutations, they are necessarily (albeit by implication, rather than by explicit declaration) talking about what sorts of mutations are or are not possible. For instance, take the claim "mutations cannot create information". This is equivalent to the claim "no mutation can transform a genetic sequence with X amount of information into a different genetic sequence with (X+N) amount of information". And that claim, if true, puts restrictions on what sort of mutation-induced changes in genetic sequence are possible! We could determine whether or not a particular case of cancer was due to genetic mutation by sequencing the patient's own DNA, then sequencing the DNA from one of the patient's tumors, and finally measuring the information content of DNA from both sources. We could make genetically-modified organisms which are all but completely immune to mutation, because we constructed their DNA to contain the lowest amount of information consistent with being a functioning life-form...Now do you see why we ought to care about IDiot/Creationist claims re: 'information' and evolutionary biology, if those claims actually were true?

Quote

To me all this information stuff is just as bogus as the argument based on the SLoT.

Hey, I agree with you 100%! I just like to play with counterfactuals; in this case, take an IDiot/Creationist claim at face value, and see what the consequences of that claim are.

However for all the millions of questions that have been answered not a single answer has turned out to be "intelligent design".

So, while a good scientist will not, cannot, rule out "ID" as a possible explanation as yet there is no actual evidence for ID at all and so no reason to consider it as an explanation for anything at all.

Sure, some people believe that evolution is insufficient to explain the diversity of life we see around us, but they are unable to provide an alternative with *any* explanatory power whatsoever.

So the question asked in that paper is:

Quote

How does mutation-induced variation in a molecular network generate variation in the resulting phenotype?

Yet it seems that ID does not even get close to a look in

Quote

The evidence for evolution itself is robust as it comes from the three independent lines that each tells thesame story: history (fossil record and isotope dating),morphology (taxonomic relationship and comparativeembryology in living organisms - evolutionary changestarts off as developmental change ) and molecularsequence relationships.

So whatever the evolutionary synthesis becomes in order to be able to answer these questions satisfactory I'd not bet that ID would have anything to do with it, no matter how long you wait.

Does that help?

--------------I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies".FTK

if there are even critical flaws in Gauger’s work, the evo mat narrative cannot standGordon Mullings

The evolutionary synthesis, the standard 20th century view of how evolutionary change occurs, is based on selection, heritable phenotypic variation and a very simple view of genes. It is therefore unable to incorporate two key aspects of modern molecular knowledge

How does that follow? The evolutionary synthesis doesn't make any assumption on the simplicity of genes and their link to phenotypes, and even what's the source of the variation (mutation, methylation). Quantitative genetics is a solid discipline. There is heritable phenotypic variation and non-heritable variation, with epistasis, dominance, maternal effects... all being complex, but factored in the equations. Only heritability (narrow sense) is subject to natural selection. Simple as that. So the neo-lamarkians should show how the newly discovered mechanisms (methylation, etc) integrate into the equations, before claiming that they overturn the current theory. So far, I haven't seen how epigenetic is supposed to affect evolution. Has anyone got a good review?

and click on the abiogenesis link in the right hand column under 'categories'.

I enjoy studying abiogenesis and there are literally 100s of new articles published every year. I've got many links, reviews, etc.

One thing about abiogenesis, it is simple to falsify. All someone has to do is show that a required chemical reaction cannot happen. In the 40+ years abiogenesis research has been going on, no one has been able to say, 'x reaction cannot happen therefore abiogenesis is impossible'.

There's a fair bit of research indicating that comets have a high level of organic compounds and it very well might be that a comet strike dumped a couple of tons of concentrated organic chemicals which got life on Earth really cooking. We will never know how it happened.

The fact that we can know it is possible and that it did happen and there is nothing (so far) that requires divine intervention is enough.

--------------Ignored by those who can't provide evidence for their claims.

How does mutation-induced variation in a molecular network generate variation in the resulting phenotype?

Again I recommend "The Probability of Life" by Kirschner and Gerhart. While the first 1/3 of it or so is kinda nebulous, the later chapters go into some fascinating explorations of this very question.

--------------"But it's disturbing to think someone actually thinks creationism -- having put it's hand on the hot stove every day for the last 400 years -- will get a different result tomorrow." -- midwifetoad

and click on the abiogenesis link in the right hand column under 'categories'.

I enjoy studying abiogenesis and there are literally 100s of new articles published every year. I've got many links, reviews, etc.

One thing about abiogenesis, it is simple to falsify. All someone has to do is show that a required chemical reaction cannot happen. In the 40+ years abiogenesis research has been going on, no one has been able to say, 'x reaction cannot happen therefore abiogenesis is impossible'.

There's a fair bit of research indicating that comets have a high level of organic compounds and it very well might be that a comet strike dumped a couple of tons of concentrated organic chemicals which got life on Earth really cooking. We will never know how it happened.

The fact that we can know it is possible and that it did happen and there is nothing (so far) that requires divine intervention is enough.

I was confused by this passage from the penultimate paragraph of Bard's review:

Quote

Complex systems have properties that cannot be pre- dicted, albeit that they can be understood with hindsight, and it may well be that the network for some trait (e.g. bone growth or pigmentation pattern) in the offspring has quantitative properties that are very different from those of the parents, not because of new mutations but because the novel mix of the rate constants will yield a trait that is an outlier of the normal distribution (known as a sport in breeding circles). As a result, the offspring may be able to colonise a novel environment far better than its peers. Equally important, this variant will naturally be heritable because it derives from the kinetics of the network (minor variation) rather than additions or losses to the proteins that comprise them.

I understand and agree that a novel combination of existing alleles could result in the offspring having a novel phenotype due to particular network interactions. But how would that novel phenotype be heritable? If it depends on an unlikely combination of alleles, it's not likely to recur in the subsequent generation.

And even if it did result in selective fixation of the relevant combination of alleles, how does that go beyond existing evolutionary theory?

[after a cursory look at that wikipage]So your Creationist buddies have a protocol by which they can measure information (don't see it, myself, but if they're citing that wikipage as providing such a protocol, they must see it, right?). Again, groovy. Your next step should be, ask them to use that information-measuring protocol to determine how much information is contained in various nucleotide sequences, particularly pairs of sequences whose information content you then compare.

Hi,

I'd like some more information on this since I have to make a standing argument.

So here are some questions that came through:

1) Why would they need to apply the definition to nuclotide sequences?2)They have other definitions of information too are they all wrong? 3) Bioinformatics works with information sciences and Biology all the time. Don't they have the same problem of defenition and measurement?4) By asking them to use their information measuring protocol - I assume you mean the stupid durston equation right? 5) Are there other ways to measure information, how would I know if he were just guessing?6) Aside from the one link supplied do you have other links that would help debunk durston?7) If you have other fav sites (asides from talkorigins that in some things is a little outdated) that debunk Idiots in general let me know. Thanks for all your help!Marty

Ps Some info on the Breed of Idiots that I have picked a fight with:1) A few are hard core nuts, most are just ordinary street people who know next to nothing about anything except tomorrow nights reality show. So alot of the stuff that I explain needs to be explained in simple terms. Giving basic examples and giving complete but information without overdoing it.2) Aside from the information theory thing. They do not supply their version. They seem to be following tactic: Show that whatever scientific theory is not certain and has problems (do this by throwing everything including the kitchen sink at them), proceed in showing that therefore scientist base their theories on faith. But since the theory is off, their faith is misplaced and esentially relies on errors. The real faith is about ecc... I'll spare you the rest. Is there a name for this spiecies of Idiot? 3) Given the above you'd say well you must have something better to do "go to a party or something". But I feel it's wrong, ordinary people are getting sucked up by this, I mean if it weren't lies it would be be okay, I mean if it makes you happy fine. But it's lies and this bothers me.4) When they run out of arguments they start insulting and saying that I don't understand and change the subject. But they can do this only a limited number of times already some ordinaries in the forum have started to show signs of saying hey she's got a point.

You guys are probaby really used to all this stuff. And my post is way to long.

Thanks... really thanks :)

--------------"Cows who know a moose when they see one will do infinitely better than a cow that pairs with a moose because they cannot see the difference either." Gary Gaulin

[after a cursory look at that wikipage]So your Creationist buddies have a protocol by which they can measure information (don't see it, myself, but if they're citing that wikipage as providing such a protocol, they must see it, right?). Again, groovy. Your next step should be, ask them to use that information-measuring protocol to determine how much information is contained in various nucleotide sequences, particularly pairs of sequences whose information content you then compare.

Hi,

I'd like some more information on this since I have to make a standing argument.

So here are some questions that came through:

1) Why would they need to apply the definition to nuclotide sequences?2)They have other definitions of information too are they all wrong? 3) Bioinformatics works with information sciences and Biology all the time. Don't they have the same problem of defenition and measurement?4) By asking them to use their information measuring protocol - I assume you mean the stupid durston equation right? 5) Are there other ways to measure information, how would I know if he were just guessing?6) Aside from the one link supplied do you have other links that would help debunk durston?7) If you have other fav sites (asides from talkorigins that in some things is a little outdated) that debunk Idiots in general let me know. Thanks for all your help!Marty

Ps Some info on the Breed of Idiots that I have picked a fight with:1) A few are hard core nuts, most are just ordinary street people who know next to nothing about anything except tomorrow nights reality show. So alot of the stuff that I explain needs to be explained in simple terms. Giving basic examples and giving complete but information without overdoing it.2) Aside from the information theory thing. They do not supply their version. They seem to be following tactic: Show that whatever scientific theory is not certain and has problems (do this by throwing everything including the kitchen sink at them), proceed in showing that therefore scientist base their theories on faith. But since the theory is off, their faith is misplaced and esentially relies on errors. The real faith is about ecc... I'll spare you the rest. Is there a name for this spiecies of Idiot? 3) Given the above you'd say well you must have something better to do "go to a party or something". But I feel it's wrong, ordinary people are getting sucked up by this, I mean if it weren't lies it would be be okay, I mean if it makes you happy fine. But it's lies and this bothers me.4) When they run out of arguments they start insulting and saying that I don't understand and change the subject. But they can do this only a limited number of times already some ordinaries in the forum have started to show signs of saying hey she's got a point.

You guys are probaby really used to all this stuff. And my post is way to long.

Thanks... really thanks :)

If you can do a signature line at the bottom of each of your posts, then do something like this:

"Can you provide the same level of detail about your notion that you demand for science?"

Seriously, at the end of every post, ask them what their position is and list all the evidence that they have for it. They won't answer, they can't answer and it really hammers home the fact that they are basing their notions on nothing.

Here's the deal with information... it is a verifiable, mathematical quantity. It can be measured, observed, and worked with.

If they cannot provide a method for determining information (however that they wish to define it), then they are just making stuff up. You can read about Shannon information on wikipedia.

They probably keep saying something like 'evolution can't add information'. Ask them why. By what basis do they make this claim? What they are basically saying is that nothing can ever be inserted into a strand of DNA... which is demonstrably false.

Remind them that information does not equal meaning. Remind them to answer the question, which has more information 30 minutes of a churchill speech or 30 minutes of white noise.

For all of their claims, they should be able to provide a demonstration of the concepts and be able to explain it to anyone. If they cannot, then their ideas are pretty much useless. Remind them that you have a battery of people ready to help you understand the mathematics.

You can also remind them that in any observation or determination of 'information content', that given a data set and a process, then everyone from an 8th grade student to a Muslim Ph.D. should get exactly the same result. If only Christians get the correct result, then the process is biased and not valid.

Without an unbiased, repeatable test, then they are just babbling and trying to confuse the issue. Do not let them off.

If there are people who are asking questions, then encourage them to read up on information and things like insertion mutations.

Take the claims of the creationist to the next level. One thing that creationists really don't do well is think about the logical consequences of what they say. Much like the example I gave above... if information in DNA cannot increase, then insertion mutations cannot happen... since insertion mutations do happen, then information increases.

I hope that helps.

--------------Ignored by those who can't provide evidence for their claims.

[after a cursory look at that wikipage]So your Creationist buddies have a protocol by which they can measure information (don't see it, myself, but if they're citing that wikipage as providing such a protocol, they must see it, right?). Again, groovy. Your next step should be, ask them to use that information-measuring protocol to determine how much information is contained in various nucleotide sequences, particularly pairs of sequences whose information content you then compare.

Hi,

I'd like some more information on this since I have to make a standing argument.

So here are some questions that came through:

1) Why would they need to apply the definition to nuclotide sequences?

Because nucleotide sequences are the (figurative) book in which this 'genetic information' stuff is (figuratively) written. So if they can't apply their definition to nucleotide sequences, "information"-as-defined-by-them isn't important or relevant to evolution.

Quote

2)They have other definitions of information too are they all wrong?

Yes, there are a number of different definitions of 'information'. Generally speaking, it's just a good idea to specify which definition you're using in the first place, because it helps to avoid confusion. And in the context of the Creationism/evolution argument, it's really a good idea, because by some definitions of 'information', random changes can create new 'information'! So when a Creationist makes noise about how random mutations can't create new information, get them to nail down exactly which definition of 'information' they're using, because (a) it avoids confusion, and (b) if they're using one of the 'information'-definitions under which random mutations can create the stuff, you can nail their lying arse to the wall.

Quote

3) Bioinformatics works with information sciences and Biology all the time. Don't they have the same problem of defenition and measurement?

Yes, real scientists who work with information do need to be clear about which definition of 'information' they're using, and how they measure it. Fortunately, real scientists are clear about these things, so it's not a problem for real scientists.

Quote

4) By asking them to use their information measuring protocol - I assume you mean the stupid durston equation right?

If that's what they claim to be using, yes. If they change their minds and decide "uh, no, the Durston thing isn't what we mean", then insist on their specifying what they do mean. Do not let them get away with vague, formless assertions; insist on specific details.

Quote

5) Are there other ways to measure information, how would I know if he were just guessing?

If they can tell you the method by which they're measuring information, you don't need to guess -- you can use that method to confirm their answer for yourself. And if they can't tell you the method by which they're measuring information, you get to pound on them for not knowing what the fuck they're talking about.

I was confused by this passage from the penultimate paragraph of Bard's review:

Quote

Complex systems have properties that cannot be pre- dicted, albeit that they can be understood with hindsight, and it may well be that the network for some trait (e.g. bone growth or pigmentation pattern) in the offspring has quantitative properties that are very different from those of the parents, not because of new mutations but because the novel mix of the rate constants will yield a trait that is an outlier of the normal distribution (known as a sport in breeding circles). As a result, the offspring may be able to colonise a novel environment far better than its peers. Equally important, this variant will naturally be heritable because it derives from the kinetics of the network (minor variation) rather than additions or losses to the proteins that comprise them.

I understand and agree that a novel combination of existing alleles could result in the offspring having a novel phenotype due to particular network interactions. But how would that novel phenotype be heritable? If it depends on an unlikely combination of alleles, it's not likely to recur in the subsequent generation.

And even if it did result in selective fixation of the relevant combination of alleles, how does that go beyond existing evolutionary theory?

I feel like I must be missing something, but I'm not sure what.

I guess we should really answer this question:

how does mutation-induced variation in a molecular network generate variation in the resulting phenotype? At least in some detail if we are to trash the book review

or am I missing something

Marty

--------------"Cows who know a moose when they see one will do infinitely better than a cow that pairs with a moose because they cannot see the difference either." Gary Gaulin

Shapiro plays at being L'enfant terrible, but he doesn't seem stupid enough to assert that variation anticipates need.

He seems to take an extreme position on evolvability and seems to assert that there are mechanisms to increase certain kinds of mutations as a response to stress.

There are in bacteria. Under heat stress, or antibiotic attack, error checking during DNA replication is turned (nearly) off in bacteria (and archaea?) generating huge mutation rates.

This could be why bacteria are so successful. But, this approach would obviously destroy any metazoans.

There are certainly mechanisms that increase mutation rates under stress. But is there evidence that such increased mutation is actually adaptive? Or is it merely an unavoidable consequence of things like needing to relax proofreading in order to replicate damaged DNA?

Shapiro definitely thinks it's adaptive. He even goes so far as to claim that:

Quote

Large-scale genome-wide reorganizations occur rapidly (potentially within a single generation) following activation of natural genetic engineering systems in response to a major evolutionary challenge. The cellular regulation of natural genetic engineering automatically imposes a punctuated tempo on the process of evolutionary change.

This does seem to flirt with ideas like front loading and purposeful evolution. Perhaps he's merely being excessively metaphorical, but I don't see any sense in which individual organisms can be properly described as responding to evolutionary challenge.

He also ignores the seemingly insurmountable issue of how such mechanisms could apply to large organisms. Individual cells in our bodies might respond to stress in some of the ways Shapiro suggests, but there's no known mechanism to allow "successful" responses in a somatic cell to be transmitted to the germ cells.